def calculate_climatology(suffix = "relax", start_year = 1981, end_year = 2010, period = "both", do3hr = False, doQC = False, doBC = False):
'''
Make 1x1 pentad climatology
:param str suffix: "relax" or "strict" criteria
:param int start_year: start year to process
:param int end_year: end year to process
:param str period: which period to do day/night/both?
:param bool do3hr: run on 3hr --> pentad data
:param bool doQC: incorporate the QC flags or not
:param bool doBC: work on the bias corrected data
:returns:
'''
settings = set_paths_and_vars.set(doBC = doBC, doQC = doQC)
if suffix == "relax":
N_YEARS_PRESENT = 10 # number of years present to calculate climatology
elif suffix == "strict":
N_YEARS_PRESENT = 15 # number of years present to calculate climatology
print "Do 3hrly: {}".format(do3hr)
N_YEARS = end_year - start_year + 1
# read in each variable - memory issues
all_clims = np.ma.zeros([len(OBS_ORDER), 73, len(grid_lats), len(grid_lons)])
# KW - why set up as np.ones?
all_clims.mask = np.zeros([len(OBS_ORDER), 73, len(grid_lats), len(grid_lons)])
all_stds = np.ma.zeros([len(OBS_ORDER), 73, len(grid_lats), len(grid_lons)])
all_stds.mask = np.zeros([len(OBS_ORDER), 73, len(grid_lats), len(grid_lons)])
# KW no mask??? I've set one with fill_value as -1 - should the mask be .zeros or .ones though?
all_n_obs = np.ma.zeros([N_YEARS, 73, len(grid_lats), len(grid_lons)])
all_n_obs.mask = np.zeros([N_YEARS, 73, len(grid_lats), len(grid_lons)])
all_n_obs.fill_value = -1
for v, var in enumerate(OBS_ORDER):
print var.name
# number of pentads = 365/5 = 73
# set up empty data array
all_pentads = np.ma.zeros([N_YEARS, 73, len(grid_lats), len(grid_lons)])
# sets up a mask of 'False' = not masked!
all_pentads.mask = np.zeros([N_YEARS, 73, len(grid_lats), len(grid_lons)])
all_pentads.fill_value = settings.mdi
# read in relevant years
for y, year in enumerate(np.arange(start_year, end_year + 1)):
print year
if do3hr:
filename = settings.DATA_LOCATION + "{}_1x1_pentad_from_3hrly_{}_{}_{}.nc".format(settings.OUTROOT, year, period, suffix)
else:
filename = settings.DATA_LOCATION + "{}_1x1_pentad_{}_{}_{}.nc".format(settings.OUTROOT, year, period, suffix)
ncdf_file = ncdf.Dataset(filename,'r', format='NETCDF4')
all_pentads[y, :, :, :] = ncdf_file.variables[var.name][:]
if v == 0:
all_n_obs[y, :, :, :] = ncdf_file.variables["n_obs"][:]
# years x pentads x lats x lons
n_grids = np.ma.count(all_pentads, axis = 0)
# collapse down the years
if settings.doMedian:
all_clims[v, :, :, :] = utils.bn_median(all_pentads, axis = 0)
else:
all_clims[v, :, :, :] = np.ma.mean(all_pentads, axis = 0)
all_stds[v, :, :, :] = np.ma.std(all_pentads, axis = 0)
# mask where fewer than 50% of years have data
locs = np.ma.where(n_grids < N_YEARS_PRESENT)
all_clims[v, :, :, :].mask[locs] = True
# KW should probably mask stdev too - although unmasked it does show the potential coverage
all_stds[v, :, :, :].mask[locs] = True
if settings.plots and v == 0:
import matplotlib.pyplot as plt
plt.clf()
plt.hist(n_grids.reshape(-1), bins = np.arange(-1,32), align = "left", log = True, rwidth=0.5)
plt.axvline(x = N_YEARS_PRESENT-0.5, color = "r")
plt.title("Number of years present in each pentad")
plt.xlabel("Number of years (max = 30)")
plt.ylabel("Frequency (log scale)")
plt.savefig(settings.PLOT_LOCATION + "pentad_clims_n_years_{}_{}_{}.png".format(year, period, suffix))
# now process number of observations (KW all_n_obs wasn't a masked array - so have set it up as one - BUT not really convinced this
# is working as it should. No import numpy.ma?
all_obs = np.ma.sum(all_n_obs, axis = 0)
# set up time array
times = utils.TimeVar("time", "time since 1/1/{} in days".format(1), "days", "time")
times.data = np.arange(0, 73) * 5
# write files
if do3hr:
out_filename = settings.DATA_LOCATION + settings.OUTROOT + "_1x1_pentad_climatology_from_3hrly_{}_{}.nc".format(period, suffix)
else:
out_filename = settings.DATA_LOCATION + settings.OUTROOT + "_1x1_pentad_climatology_{}_{}.nc".format(period, suffix)
utils.netcdf_write(out_filename, all_clims, n_grids, all_obs, OBS_ORDER, grid_lats, grid_lons, times, frequency = "P")
if do3hr:
out_filename = settings.DATA_LOCATION + settings.OUTROOT + "_1x1_pentad_stdev_from_3hrly_{}_{}.nc".format(period, suffix)
else:
out_filename = settings.DATA_LOCATION + settings.OUTROOT + "_1x1_pentad_stdev_{}_{}.nc".format(period, suffix)
utils.netcdf_write(out_filename, all_stds, n_grids, all_obs, OBS_ORDER, grid_lats, grid_lons, times, frequency = "P")
# test distribution of obs with grid boxes
if do3hr:
outfile = file(settings.OUTROOT + "_1x1_pentad_climatology_from_3hrly_{}_{}.txt".format(period, suffix), "w")
else:
outfile = file(settings.OUTROOT + "_1x1_pentad_climatology_{}_{}.txt".format(period, suffix), "w")
utils.boxes_with_n_obs(outfile, all_obs, all_clims[0], N_YEARS_PRESENT)
return # calculate_climatology
def calculate_climatology(suffix = "relax", start_year = 1981, end_year = 2010, period = "both", daily = False,
doQC = False, doQC1it = False, doQC2it = False, doQC3it = False,
doBC = False, doBCtotal = False, doBChgt = False, doBCscn = False):
#def calculate_climatology(suffix = "relax", start_year = 1981, end_year = 2010, period = "both", daily = False, doQC = False, doBC = False):
# end
'''
Make 5x5 monthly climatology
:param str suffix: "relax" or "strict" criteria
:param int start_year: start year to process
:param int end_year: end year to process
:param str period: which period to do day/night/both?
:param bool daily: run in 1x1 daily --> 5x5 monthly data
:param bool doQC: incorporate the QC flags or not
# KATE modified
:param bool doQC1it: incorporate the 1st iteration QC flags or not
:param bool doQC2it: incorporate the 2nd iteration QC flags or not
:param bool doQC3it: incorporate the 3rd iteration QC flags or not
# end
:param bool doBC: work on the bias corrected data
# KATE modified
:param bool doBCtotal: work on the bias corrected data
:param bool doBChgt: work on the height only bias corrected data
:param bool doBCscn: work on the screen only bias corrected data
# end
:returns:
'''
# KATE modified
settings = set_paths_and_vars.set(doBC = doBC, doBCtotal = doBCtotal, doBChgt = doBChgt, doBCscn = doBCscn, doQC = doQC, doQC1it = doQC1it, doQC2it = doQC2it, doQC3it = doQC3it)
#settings = set_paths_and_vars.set(doBC = doBC, doQC = doQC)
# end
if suffix == "relax":
N_YEARS_PRESENT = 10 # number of years present to calculate climatology
elif suffix == "strict":
N_YEARS_PRESENT = 15 # number of years present to calculate climatology
print "Do daily: {}".format(daily)
N_YEARS = end_year - start_year + 1
# read in each variable - memory issues
all_clims = np.ma.zeros([len(OBS_ORDER), 12, len(grid_lats), len(grid_lons)])
# KW - why set up as np.ones?
all_clims.mask = np.zeros([len(OBS_ORDER), 12, len(grid_lats), len(grid_lons)])
all_stds = np.ma.zeros([len(OBS_ORDER), 12, len(grid_lats), len(grid_lons)])
all_stds.mask = np.zeros([len(OBS_ORDER), 12, len(grid_lats), len(grid_lons)])
# KW no mask??? I've set one with fill_value as -1 - should the mask be .zeros or .ones though?
all_n_obs = np.ma.zeros([N_YEARS * 12, len(grid_lats), len(grid_lons)])
all_n_obs.mask = np.zeros([N_YEARS * 12, len(grid_lats), len(grid_lons)])
all_n_obs.fill_value = -1
if daily:
filename = settings.DATA_LOCATION + "{}_5x5_monthly_from_daily_{}_{}.nc".format(settings.OUTROOT, period, suffix)
else:
filename = settings.DATA_LOCATION + "{}_5x5_monthly_{}_{}.nc".format(settings.OUTROOT, period, suffix)
ncdf_file = ncdf.Dataset(filename,'r', format='NETCDF4')
times = ncdf_file.variables["time"]
data_start = int(times.long_name.split(" ")[2].split("/")[-1])
clim_offset = (start_year - data_start) * 12
for v, var in enumerate(OBS_ORDER):
print var.name
# number of pentads = 365/5 = 73
# set up empty data array
all_months = np.ma.zeros([N_YEARS * 12, len(grid_lats), len(grid_lons)])
# sets up a mask of 'False' = not masked!
all_months.mask = np.zeros([N_YEARS * 12, len(grid_lats), len(grid_lons)])
all_months.fill_value = settings.mdi
all_months[:, :, :] = ncdf_file.variables[var.name][clim_offset:clim_offset + (30*12)]
# months x lats x lons
shape = all_months.shape
all_months = all_months.reshape(-1, 12, shape[-2], shape[-1])
n_grids = np.ma.count(all_months, axis = 0)
# collapse down the years
# KATE MEDIAN WATCH
# KATE modified - forced to use MEAN
all_clims[v, :, :, :] = np.ma.mean(all_months, axis = 0)
#if settings.doMedian:
# all_clims[v, :, :, :] = utils.bn_median(all_months, axis = 0)
#else:
# all_clims[v, :, :, :] = np.ma.mean(all_months, axis = 0)
# end
all_stds[v, :, :, :] = np.ma.std(all_months, axis = 0)
# mask where fewer than 50% of years have data
locs = np.ma.where(n_grids < N_YEARS_PRESENT)
all_clims[v, :, :, :].mask[locs] = True
# KW should probably mask stdev too - although unmasked it does show the potential coverage
all_stds[v, :, :, :].mask[locs] = True
if settings.plots and v == 0:
import matplotlib.pyplot as plt
plt.clf()
plt.hist(n_grids.reshape(-1), bins = np.arange(-1,32), align = "left", log = True, rwidth=0.5)
plt.axvline(x = N_YEARS_PRESENT-0.5, color = "r")
plt.title("Number of years present in each pentad")
plt.xlabel("Number of years (max = 30)")
plt.ylabel("Frequency (log scale)")
plt.savefig(settings.PLOT_LOCATION + "monthly_5x5_clims_n_years_{}_{}.png".format(period, suffix))
# now process number of observations (KW all_n_obs wasn't a masked array - so have set it up as one - BUT not really convinced this
# is working as it should. No import numpy.ma?
all_n_obs[:, :, :] = ncdf_file.variables["n_obs"][clim_offset:clim_offset + (30*12)]
all_n_obs = all_n_obs.reshape(-1, 12, shape[-2], shape[-1])
all_obs = np.ma.sum(all_n_obs, axis = 0)
# set up time array
times = utils.TimeVar("time", "time since 1/1/{} in days".format(1), "days", "time")
month_lengths = [calendar.monthrange(1, x + 1)[1] for x in range(12)]
times.data = [sum(month_lengths[0:x]) for x in range(12)]
# write files
if daily:
out_filename = settings.DATA_LOCATION + settings.OUTROOT + "_5x5_monthly_climatology_from_daily_{}_{}.nc".format(period, suffix)
else:
out_filename = settings.DATA_LOCATION + settings.OUTROOT + "_5x5_monthly_climatology_{}_{}.nc".format(period, suffix)
# KATE modified - only outputting 90 to -90 now and have changed grid_lats above
utils.netcdf_write(out_filename, all_clims, n_grids, all_obs, OBS_ORDER, grid_lats, grid_lons, times, frequency = "Y")
#if period == "both":
# utils.netcdf_write(out_filename, all_clims, n_grids, all_obs, OBS_ORDER, grid_lats[::-1], grid_lons, times, frequency = "Y")
#else:
# utils.netcdf_write(out_filename, all_clims, n_grids, all_obs, OBS_ORDER, grid_lats, grid_lons, times, frequency = "Y")
# end
if daily:
out_filename = settings.DATA_LOCATION + settings.OUTROOT + "_5x5_monthly_stdev_from_daily_{}_{}.nc".format(period, suffix)
else:
out_filename = settings.DATA_LOCATION + settings.OUTROOT + "_5x5_monthly_stdev_{}_{}.nc".format(period, suffix)
# KATE modified - only outputting 90 to -90 now and have changed grid_lats above
utils.netcdf_write(out_filename, all_stds, n_grids, all_obs, OBS_ORDER, grid_lats, grid_lons, times, frequency = "Y")
#if period == "both":
# utils.netcdf_write(out_filename, all_stds, n_grids, all_obs, OBS_ORDER, grid_lats[::-1], grid_lons, times, frequency = "Y")
#else:
# utils.netcdf_write(out_filename, all_stds, n_grids, all_obs, OBS_ORDER, grid_lats, grid_lons, times, frequency = "Y")
# end
# test distribution of obs with grid boxes
if daily:
outfile = file(settings.OUTROOT + "_5x5_monthly_climatology_from_daily_{}_{}.txt".format(period, suffix), "w")
else:
outfile = file(settings.OUTROOT + "_5x5_monthly_climatology_{}_{}.txt".format(period, suffix), "w")
utils.boxes_with_n_obs(outfile, all_obs, all_clims[0], N_YEARS_PRESENT)
return # calculate_climatology
def do_merge(fileroot, mdi, suffix = "relax", clims = False, doMedian = False):
'''
Merge the _day and _night files
Do a np.ma.mean or median for the data and a sum for the n_obs and n_grids
Output with a _both suffix
:param str fileroot: root for filenames
:param flt mdi: missing data indicator
:param str suffix: "relax" or "strict" criteria
:param bool clims: if climatologies then don't try and process anomalies.
'''
OBS_ORDER = utils.make_MetVars(mdi, multiplier = False)
if clims:
# KW make OBS_ORDER only the actual variables - remove anomalies
NEWOBS_ORDER = []
for v, var in enumerate(OBS_ORDER):
if "anomalies" not in var.name:
NEWOBS_ORDER.append(var)
del OBS_ORDER
OBS_ORDER = np.copy(NEWOBS_ORDER)
del NEWOBS_ORDER
# spin through both periods
for p, period in enumerate(["day", "night"]):
print period
# go through the variables
for v, var in enumerate(OBS_ORDER):
print " {}".format(var.name)
ncdf_file = ncdf.Dataset("{}_{}_{}.nc".format(fileroot, period, suffix),'r', format='NETCDF4')
if v == 0 and p == 0:
shape = list(ncdf_file.variables[var.name][:].shape)
shape.insert(0, len(OBS_ORDER)+2) # add all the variables
shape.insert(0, 2) # insert extra dimension to allow day + night
all_data = np.ma.zeros(shape)
all_data[p, v] = ncdf_file.variables[var.name][:]
# get lats/lons of box centres
lat_centres = ncdf_file.variables["latitude"]
# KATE modified - this results in lats that go from 92.5 to -82,5 so I've switched the + for a -
latitudes = lat_centres - (lat_centres[1] - lat_centres[0])/2.
#latitudes = lat_centres + (lat_centres[1] - lat_centres[0])/2.
# end
lon_centres = ncdf_file.variables["longitude"]
longitudes = lon_centres + (lon_centres[1] - lon_centres[0])/2.
# get times - make a dummy object and then populate attributes
times = utils.TimeVar("time", "time since 1/{}/{} in hours".format(1, 1973), "hours", "time")
times.long_name = ncdf_file.variables["time"].long_name
times.standard_name = ncdf_file.variables["time"].standard_name
times.long_name = ncdf_file.variables["time"].long_name
times.units = ncdf_file.variables["time"].units
times.data = ncdf_file.variables["time"][:]
else:
all_data[p, v] = ncdf_file.variables[var.name][:]
# and get n_obs and n_grids
all_data[p, -2] = ncdf_file.variables["n_grids"][:]
all_data[p, -1] = ncdf_file.variables["n_obs"][:]
# invert latitudes
latitudes = latitudes[::-1]
all_data = all_data[:,:,:,::-1,:]
# got all the info, now merge
if doMedian:
merged_data = utils.bn_median(all_data[:, :len(OBS_ORDER)], axis = 0)
else:
merged_data = np.ma.mean(all_data[:, :len(OBS_ORDER)], axis = 0)
# and process the grids and observations (split off here so have incorporated latitude inversion)
n_grids = np.ma.sum(all_data[:, -2], axis = 0)
n_obs = np.ma.sum(all_data[:, -1], axis = 0)
n_obs.fill_value = -1
n_grids.fill_value = -1
# write the output file
utils.netcdf_write("{}_{}_{}.nc".format(fileroot, "both", suffix), merged_data, n_grids, n_obs, OBS_ORDER, latitudes, longitudes, times, frequency = "P")
# test distribution of obs with grid boxes
outfile = file("{}_{}_{}.txt".format(fileroot.split("/")[-1], "both", suffix), "w")
utils.boxes_with_n_obs(outfile, n_obs, merged_data[0], "")
return # do_merge
